The isolation of microorganisms in pure culture has established a solid foundation of the metabolic capabilities of microorganisms, which has allowed us to understand key transformation processes in nature as well as in microbial biochemistry and molecular biology. This chapter focuses on trophic interactions involving microbes and food webs as revealed by stable isotope probing (SIP) of nucleic acids and also highlights studies using related techniques where exceptional insights have been gained in delineating trophic interactions. The concept of cooperation in anaerobic degradation of organic matter is briefly introduced to facilitate an understanding of carbon flow and trophic interactions in the anaerobic microbial food chain that is governed by both specialization of the key players and thermodynamic constraints. The thermodynamic constraints on fatty acid oxidations provide a biogeochemical framework which renders only syntrophic secondary fermenters capable of dissimilation and assimilation: only syntrophic coupling of fatty acid-oxidizing and hydrogen- and acetate-scavenging reactions makes fatty acid oxidation under methanogenic conditions exergonic. A number of studies have shown how carbon (and nitrogen) flow can be traced through microbial communities and food webs via phylogenetically identified microbes and higher-trophic-level consumers by using nucleic acid SIP and novel single-cell-based approaches of SIP.

Ratios of substrate dissimilation and assimilation in anaerobic microorganisms thriving on sugars. Left: 13C-substrate-metabolizing population. Right: population metabolizing a nonlabeled substrate. It is assumed that the central metabolite pool of both populations originates from the energy substrate. Coassimilation of a 13C-labeled substrate by a potential cross-feeder (right) will most likely result in label dilution due to catabolism of the unlabeled energy substrate (further explanations in the text).

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FIGURE 3

Ratios of substrate dissimilation and assimilation in anaerobic microorganisms thriving on sugars. Left: 13C-substrate-metabolizing population. Right: population metabolizing a nonlabeled substrate. It is assumed that the central metabolite pool of both populations originates from the energy substrate. Coassimilation of a 13C-labeled substrate by a potential cross-feeder (right) will most likely result in label dilution due to catabolism of the unlabeled energy substrate (further explanations in the text).